The scheme is supported by the Muslim Council of Scotland, which has been highlighting the risk of travellers contracting the disease on the annual pilgrimage to Mecca.
Reach Pharmacy will head the initiative in its chains in Eastwood, Argyle Street and Hillhead Street.
Hanzala Malik MSP said: "Local pharmacies will be able to offer this vaccination direct to travellers. It will be convenient and cost effective, as it will be offered at a special rate.
"I am delighted that Reach Pharmacy has been appointed as a partner clinic, particularly as its pharmacies are easily accessible and have staff fluent in English, Urdu and Punjabi.
"I would urge all travellers to Mecca to protect themselves and their family and friends."
Neeraj Salwan of Reach Pharmacy said: "A certificate of vaccination is now a requirement for the estimated 25,000 British Muslims who will travel to Hajj in 2011."
This year's pilgrimage to Mecca will take place in October/November.